[gmx-users] parallel run error

[David]

On Tue, 2004-11-23 at 12:42 -0500, Lianqing Zheng wrote:
> Thanks, David! Do I need to recompile lam, fftw, and gromacs or just
> gromacs? I did it for gromacs but still got the same error.
> 
Running 
make distclean
configure [OPTS]
make install 

should do it.

> We actually have libxml2 at /usr/lib/libxml2.so.2. It's only on
> the master node. Do I need to install it on all nodes?
Yes that would be a good solution.

> 
> Thanks,
> Lianqing
> 
> 
> On Tue, 23 Nov 2004, David wrote:
> 
> >On Tue, 2004-11-23 at 11:46 -0500, Lianqing Zheng wrote:
> >> Dear GMX-pals,
> >> 
> >> Here is what I did:
> >> 
> >> 1. Compile and install fftw
> >> a) MPICC=/opt/lam-7.0/bin/mpicc
> >> b) ./configure --prefix=/home/lzheng/fftw-2.1.3 --enable-float
> >> --enable-type-prefix --enable-mpi 
> >> c) make
> >> d) make install
> >> 
> >> 2. Compile and install gromacs 3.2.1
> >> a) export CPPFLAGS=-I/home/lzheng/fftw-2.1.3/include
> >> b) export LDFLAGS=-L/home/lzheng/fftw-2.1.3/lib
> >> c) ./configure --prefix=/home/lzheng/gromacs-3.2.1 --enable-mpi
> >> --without-motif-libraries --without-motif-includes --without-x 
> >> d) make
> >> e) make install
> >> 
> >> 3. Run water simulation in tutorial
> >> a) lamboot -v bhost.def
> >> b) grompp -f grompp.mdp -p water.top -c spc216.gro -o water.tpr -np 4
> >> c) /opt/lam-7.0/bin/mpirun n21-24
> >> /home/lzheng/gromacs-3.2.1/i686-pc-linux-gnu/bin/mdrun  -s water.tpr -o
> >> water.trr -c water_out.gro -v -g water.log -np 4
> >> 
> >> OK, then I got the following error message:
> >> 
> >> ****begin****
> >> /home/lzheng/gromacs-3.2.1/i686-pc-linux-gnu/bin/mdrun: error while
> >> loading shared libraries: libxml2.so.2: cannot open shared object file: No
> >> such file or directory
> >Your cluster does not have libxml2 installed. Either ask your sysadm to
> >install libxml2 or configure --without-libxml2
> >
> >Note that xml may become obligatory in the next (4.0) release.
> >
> >> /home/lzheng/gromacs-3.2.1/i686-pc-linux-gnu/bin/mdrun: error while
> >> loading shared libraries: libxml2.so.2: cannot open shared object file: No
> >> such file or directory
> >> /home/lzheng/gromacs-3.2.1/i686-pc-linux-gnu/bin/mdrun: error while
> >> loading shared libraries: libxml2.so.2: cannot open shared object file: No
> >> such file or directory
> >> /home/lzheng/gromacs-3.2.1/i686-pc-linux-gnu/bin/mdrun: error while
> >> loading shared libraries: libxml2.so.2: cannot open shared object file: No
> >> such file or directory
> >> -----------------------------------------------------------------------------
> >> It seems that [at least] one of the processes that was started with
> >> mpirun did not invoke MPI_INIT before quitting (it is possible that
> >> more than one process did not invoke MPI_INIT -- mpirun was only
> >> notified of the first one, which was on node n0).
> >> 
> >> mpirun can *only* be used with MPI programs (i.e., programs that
> >> invoke MPI_INIT and MPI_FINALIZE).  You can use the "lamexec" program
> >> to run non-MPI programs over the lambooted nodes.
> >> -----------------------------------------------------------------------------
> >> ****end****
> >> 
> >> I also tried mpirun -np 4 and got the same error.
> >> 
> >> Thanks for your kind help!
> >> 
> >> Lianqing
> >> 
> >> _______________________________________________
> >> gmx-users mailing list
> >> gmx-users at gromacs.org
> >> http://www.gromacs.org/mailman/listinfo/gmx-users
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> >-- 
> >David.
> >________________________________________________________________________
> >David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
> >Dept. of Cell and Molecular Biology, Uppsala University.
> >Husargatan 3, Box 596,          75124 Uppsala, Sweden
> >phone:  46 18 471 4205          fax: 46 18 511 755
> >spoel at xray.bmc.uu.se    spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
> >++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
> >
> >_______________________________________________
> >gmx-users mailing list
> >gmx-users at gromacs.org
> >http://www.gromacs.org/mailman/listinfo/gmx-users
> >Please don't post (un)subscribe requests to the list. Use the 
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> >
> 
> _______________________________________________
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-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,          75124 Uppsala, Sweden
phone:  46 18 471 4205          fax: 46 18 511 755
spoel at xray.bmc.uu.se    spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++